Enterprises compete keenly against domestic and foreign companies. They are under strong pressure to reduce physical distribution cost to survive the competition. Major inter-business methods to achieve it are accommodation, joint ship allocation, and as their ultimate form, companies merger. But in physical distribution process a lot of factors, for example means of transport, factories, storage facilities, markets, and other external environment effect each other dynamically. Therefore it is diffcult to evaluate the methods' various effects comprehensively, quantitatively, and accurately. We think the difficulty is one of major obstacles to improve the distribution systems. This paper deals with domestic maritime cement transportation as an example. First, we develop compute simulation of physical distribution routine. Secondly, we model industry cooperation of logistics and develop ship allocation algorism and effects estimation system. Lastly, we execute several case-studies and discuss the cooperation's effects on logistics.